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its possibly the security system has been locked down by the flattened battery
I'd suggest to 1st check if your new battery has at least 12V with the engine off if it does then check that main battery connections are tight and clean and if the large fuses on the battery positive terminals are intact
if thats all OK then try replacing the battery in the key-fob and if the car is a push button start model then touch the metal portion of the key fob onto the metal outside of the push button
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glad to have helped
if you wouldn't mind rating then that would be much appreciated